A new study published in Nature unveils the mysterious world of microbial life shaping the rivers that millions of Americans depend on for drinking water. The research spans waterways across the continental United States, from small mountain streams to major rivers like the Mississippi.
“People used to think of rivers almost just as pipes, a way to move water from one place to another,” Mikayla Borton lead author on the paper and professor at Colorado State University (CSU) said in a statement. “But rivers are much more than that — they’re performing all kinds of activities. And there’s a pattern to it; those activities can be predicted.”
The research examined rivers across 19 major watershed regions, spanning diverse landscapes from the Everglades to the Western Cordillera mountains, and from Mediterranean California to the Atlantic Highlands. Scientists collected samples from rivers of various sizes, including small headwater streams and larger waterways up to sections of the Mississippi River.
To gather samples across this vast network, researchers used two complementary methods. One utilized a scientific network called The Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS), which mailed sampling kits to volunteer researchers. These kits included materials and step-by-step instructions to ensure consistent sample collection. The second method partnered with the US Geological Survey’s National Water Quality Network, which regularly monitors water quality at important river locations across America.
“It is extremely gratifying to have built something that will benefit a lot of folks beyond our team,” said James Stegen, a study co-author from Pacific Northwest National Laboratory. All water samples were processed in the same way at designated laboratories, ensuring results could be compared across different rivers. The information was compiled into a new database called Genome Resolved Open Watersheds database (GROWdb).
Researchers found that microbes significantly shape water quality through their interactions with contaminants, including antibiotics, microplastics, and agricultural runoff. Near wastewater treatment plants, researchers found elevated levels of antibiotic resistance genes, adding new evidence about the impact of human activities on river systems.
“When we look at how the land around a river is managed, we can see the processing of certain kinds of anthropogenic contaminants or chemicals through the microbes in their DNA,” said Kelly Wrighton, a professor in CSU’s College of Agricultural Sciences and study co-author. “There’s a very strong relationship. [I]t suggests there’s a signal in the microbiome of how we’re living on and managing the land that is perpetuated into the river system and then downstream.”
The study showed that microbial communities change predictably as rivers flow from small headwaters to larger waterways, with different types of microbes specializing in processing different forms of carbon and nutrients.
The study found that among thousands of different microbes in rivers, six specific types showed up everywhere they looked, from small streams to big rivers. All six use sunlight to make energy, similar to how plants photosynthesize. Think of them as tiny solar panels floating in every river studied.
The size of the river turned out to be important in determining which microbes live there. Whether a river was in the north or south (latitude) or how much carbon was in the water mattered less than simply how big the river was. As rivers get bigger, growing from small mountain streams into larger waterways, the microbial communities change in predictable ways.
In small streams (low-order rivers), researchers found microbes that specialize in breaking down complex materials like plant polymers, aromatic compounds and sugars, materials that wash in from the surrounding land. Small streams are closely connected to the land around them, often shaded by trees that drop leaves and other organic matter into the water.
As rivers grow larger (higher-order rivers), the microbial communities shift. More microbes appear that can use simpler carbon compounds, particularly methylotrophs that can process methanol. This methanol likely comes from different sources than in small streams. It is produced by river algae or when microbes break down plant materials.
The study showed this wasn’t a random change. The researchers consistently found more polymer and sugar-processing microbes in small streams, while methylotrophs dominated in larger rivers. This pattern repeated across different regions, suggesting it’s a fundamental feature of how rivers work as they grow from headwaters to major waterways.
Temperature also plays a crucial role in which microbes thrive. The researchers found a clear pattern: microbes that use sunlight for energy and those that need oxygen were strongly affected by water temperature. This suggests that as climate change alters river temperatures, it could disrupt these microbial communities that help keep rivers healthy.
The research demonstrates that river health depends on complex interactions at the microscopic level. As climate patterns change and human activities continue to impact waterways, this new knowledge about microbial communities could help scientists monitor and protect these essential water sources that millions of Americans depend on daily.
“Our hope is that this information can eventually be used to develop new diagnostics that are indicators of a healthy river versus an unhealthy river,” said Wrighton.
